I’ve used this from IBM when upgrading from v5r2 and v5r3 to v5r4:
No one can tell you what you need to know or need to do because no one else knows your environment. We don’t know your hardware nor your history of software maintenance nor what products you have installed (including which products are important for your business.)
In general, you need to plan first for a V5R3 to V5R4 upgrade. You should review important documents such as the V5R4 Memo to Users in order to learn about (and plan and prepare for) changes that were brought by V5R4.
Then you need to do the same for V6R1. If you only review V6R1, you won’t know about how V5R4 may have changed products that you use.
The above link should get you to everything you need eventually. It might require a lot of study though. There are more focused links you can use as guides while using the above link for digging into details as needed.
This planning link gets you to a lot of places. One is this Software Prerequisite page. You can also choose the Migration and upgrades link under the Planning tab.
You’ll find links there to both V6R1 and V5R4 Memos to Users as well as lots of others. The two Memos to Users may be your best sources for a starting point.